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Tank has been running for a couple months and has been cycled for about a month or so.

This evening I noticed a spot on my DG near one of his eyes, it almost looks as if a chunk of skin is missing. He also has what looks like a swollen abdomen, almost like he swallowed something big. He has a similar mark on the opposite side.

I started looking around and noticed that two of my HRs have what looks like a white thread like substance on one side of them and one side only. One of them also has what I would describe as a "flipped up" gill. It's like you can see right inside the fish.

I have moved the three of these fish to a quarantine tank until I figure out what's going on. It seems like everyone else in the tank is doing fine. All fish, including the "sick" ones have had a normal appetite.

Your tank is much too small for 6 species of fish and especially an angelfish. I agree the thread-like things are anchor worms. The flared gills could be ammonia poisoning. Perhaps not due to ammonia levels now but in the past. Could also be gill flukes. But overcrowding is not helping this situation.